1
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Yang Y, Xu B, Haverstick J, Ibtehaz N, Muszyński A, Chen X, Chowdhury MEH, Zughaier SM, Zhao Y. Differentiation and classification of bacterial endotoxins based on surface enhanced Raman scattering and advanced machine learning. NANOSCALE 2022; 14:8806-8817. [PMID: 35686584 PMCID: PMC9575096 DOI: 10.1039/d2nr01277d] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Bacterial endotoxin, a major component of the Gram-negative bacterial outer membrane leaflet, is a lipopolysaccharide shed from bacteria during their growth and infection and can be utilized as a biomarker for bacterial detection. Here, the surface enhanced Raman scattering (SERS) spectra of eleven bacterial endotoxins with an average detection amount of 8.75 pg per measurement have been obtained based on silver nanorod array substrates, and the characteristic SERS peaks have been identified. With appropriate spectral pre-processing procedures, different classical machine learning algorithms, including support vector machine, k-nearest neighbor, random forest, etc., and a modified deep learning algorithm, RamanNet, have been applied to differentiate and classify these endotoxins. It has been found that most conventional machine learning algorithms can attain a differentiation accuracy of >99%, while RamanNet can achieve 100% accuracy. Such an approach has the potential for precise classification of endotoxins and could be used for rapid medical diagnoses and therapeutic decisions for pathogenic infections.
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Affiliation(s)
- Yanjun Yang
- School of Electrical and Computer Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
| | - Beibei Xu
- Department of Statistics, The University of Georgia, Athens, GA 30602, USA
| | - James Haverstick
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA.
| | - Nabil Ibtehaz
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Xianyan Chen
- Department of Statistics, The University of Georgia, Athens, GA 30602, USA
| | - Muhammad E H Chowdhury
- Department of Electrical Engineering, College of Engineering, Qatar University, PO. Box 2713, Doha, Qatar
| | - Susu M Zughaier
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, PO. Box 2713, Doha, Qatar.
| | - Yiping Zhao
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA.
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Zhou D, Li Y, Wang X, Xie F, Chen D, Ma B, Li Y. Mesorhizobium huakuii HtpG Interaction with nsLTP AsE246 Is Required for Symbiotic Nitrogen Fixation. PLANT PHYSIOLOGY 2019; 180:509-528. [PMID: 30765481 PMCID: PMC6501076 DOI: 10.1104/pp.18.00336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 02/04/2019] [Indexed: 05/06/2023]
Abstract
Plant nonspecific lipid transfer proteins (nsLTPs) are involved in a number of biological processes including root nodule symbiosis. However, the role of nsLTPs in legume-rhizobium symbiosis remains poorly understood, and no rhizobia proteins that interact with nsLTPs have been reported to date. In this study, we used a bacteria two-hybrid system and identified the high temperature protein G (HtpG) from Mesorhizobium huakuii that interacts with the nsLTP AsE246. The interaction between HtpG and AsE246 was confirmed by far-Western blotting and bimolecular fluorescence complementation. Our results indicated that the heat shock protein 90 (HSP90) domain of HtpG mediates the HtpG-AsE246 interaction. Immunofluorescence assay showed that HtpG was colocalized with AsE246 in infected nodule cells and symbiosome membranes. Expression of the htpG gene was relatively higher in young nodules and was highly expressed in the infection zones. Further investigation showed that htpG expression affects lipid abundance and profiles in root nodules and plays an essential role in nodule development and nitrogen fixation. Our findings provide further insights into the functional mechanisms behind the transport of symbiosome lipids via nsLTPs in root nodules.
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Affiliation(s)
- Donglai Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanan Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuting Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fuli Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dasong Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Binguang Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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3
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Ma JC, Wu YQ, Cao D, Zhang WB, Wang HH. Only Acyl Carrier Protein 1 (AcpP1) Functions in Pseudomonas aeruginosa Fatty Acid Synthesis. Front Microbiol 2017; 8:2186. [PMID: 29176964 PMCID: PMC5686131 DOI: 10.3389/fmicb.2017.02186] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/25/2017] [Indexed: 11/21/2022] Open
Abstract
The genome of Pseudomonas aeruginosa contains three open reading frames, PA2966, PA1869, and PA3334, which encode putative acyl carrier proteins, AcpP1, AcpP2, and AcpP3, respectively. In this study, we found that, although these apo-ACPs were successfully phosphopantetheinylated by P. aeruginosa phosphopantetheinyl transferase (PcpS) and all holo-forms of these proteins could be acylated by Vibrio harveyi acyl-ACP synthetase (AasS), only AcpP1 could be used as a substrate for the synthesis of fatty acids, catalyzed by P. aeruginosa cell free extracts in vitro, and only acpP1 gene could restore growth in the Escherichia coliacpP mutant strain CY1877. And P. aeruginosaacpP1 could not be deleted, while disruption of acpP2 or acpP3 in the P. aeruginosa genome allowed mutant strains to grow as well as the wild type strain. These findings confirmed that only P. aeruginosa AcpP1 functions in fatty acid biosynthesis, and that acpP2 and acpP3 do not play roles in the fatty acid synthetic pathway. Moreover, disruption of acpP2 and acpP3 did not affect the ability of P. aeruginosa to produce N-acylhomoserine lactones (AHL), but replacement of P. aeruginosaacpP1 with E. coliacpP caused P. aeruginosa to reduce the production of AHL molecules, which indicated that neither P. aeruginosa AcpP2 nor AcpP3 can act as a substrate for synthesis of AHL molecules in vivo. Furthermore, replacement of acpP1 with E. coliacpP reduced the ability of P. aeruginosa to produce some exo-products and abolished swarming motility in P. aeruginosa.
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Affiliation(s)
- Jin-Cheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yun-Qi Wu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Dan Cao
- Forensic Science Center of Qingyuan, Qingyuan Public Security Department, Qingyuan, China
| | - Wen-Bin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Hong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides. mBio 2017; 8:mBio.01060-17. [PMID: 28765224 PMCID: PMC5539429 DOI: 10.1128/mbio.01060-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important for symbiosis. However, the mechanisms used by S. meliloti to resist antimicrobial activity of plant peptides are poorly understood. To address this, we applied a global genetic approach using transposon mutagenesis followed by high-throughput sequencing (Tn-seq) to identify S. meliloti genes and pathways that increase or decrease bacterial competitiveness during exposure to the well-studied cationic NCR247 peptide and also to the unrelated model antimicrobial peptide polymyxin B. We identified 78 genes and several diverse pathways whose interruption alters S. meliloti resistance to NCR247. These genes encode the following: (i) cell envelope polysaccharide biosynthesis and modification proteins, (ii) inner and outer membrane proteins, (iii) peptidoglycan (PG) effector proteins, and (iv) non-membrane-associated factors such as transcriptional regulators and ribosome-associated factors. We describe a previously uncharacterized yet highly conserved peptidase, which protects S. meliloti from NCR247 and increases competitiveness during symbiosis. Additionally, we highlight a considerable number of uncharacterized genes that provide the basis for future studies to investigate the molecular basis of symbiotic development as well as chronic pathogenic interactions. Soil rhizobial bacteria enter into an ecologically and economically important symbiotic interaction with legumes, in which they differentiate into physiologically distinct bacteroids that provide essential ammonia to the plant in return for carbon sources. Plant signal peptides are essential and specific to achieve these physiological changes. These peptides show similarity to mammalian defensin peptides which are part of the first line of defense to control invading bacterial populations. A number of these legume peptides are indeed known to possess antimicrobial activity, and so far, only the bacterial BacA protein is known to protect rhizobial bacteria against their antimicrobial action. This study identified numerous additional bacterial factors that mediate protection and belong to diverse biological pathways. Our results significantly contribute to our understanding of the molecular roles of bacterial factors during legume symbioses and, second, provide insights into the mechanisms that pathogenic bacteria may use to resist the antimicrobial effects of defensins during infections.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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6
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Bourassa DV, Kannenberg EL, Sherrier DJ, Buhr RJ, Carlson RW. The Lipopolysaccharide Lipid A Long-Chain Fatty Acid Is Important for Rhizobium leguminosarum Growth and Stress Adaptation in Free-Living and Nodule Environments. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:161-175. [PMID: 28054497 DOI: 10.1094/mpmi-11-16-0230-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Rhizobium bacteria live in soil and plant environments, are capable of inducing symbiotic nodules on legumes, invade these nodules, and develop into bacteroids that fix atmospheric nitrogen into ammonia. Rhizobial lipopolysaccharide (LPS) is anchored in the bacterial outer membrane through a specialized lipid A containing a very long-chain fatty acid (VLCFA). VLCFA function for rhizobial growth in soil and plant environments is not well understood. Two genes, acpXL and lpxXL, encoding acyl carrier protein and acyltransferase, are among the six genes required for biosynthesis and transfer of VLCFA to lipid A. Rhizobium leguminosarum mutant strains acpXL, acpXL-/lpxXL-, and lpxXL- were examined for LPS structure, viability, and symbiosis. Mutations in acpXL and lpxXL abolished VLCFA attachment to lipid A. The acpXL mutant transferred a shorter acyl chain instead of VLCFA. Strains without lpxXL neither added VLCFA nor a shorter acyl chain. In all strains isolated from nodule bacteria, lipid A had longer acyl chains compared with laboratory-cultured bacteria, whereas mutant strains displayed altered membrane properties, modified cationic peptide sensitivity, and diminished levels of cyclic β-glucans. In pea nodules, mutant bacteroids were atypically formed and nitrogen fixation and senescence were affected. The role of VLCFA for rhizobial environmental fitness is discussed.
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Affiliation(s)
- Dianna V Bourassa
- 1 Complex Carbohydrate Research Center, University of Georgia, Athens 30602, U.S.A
- 3 U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, U.S.A
| | - Elmar L Kannenberg
- 1 Complex Carbohydrate Research Center, University of Georgia, Athens 30602, U.S.A
| | - D Janine Sherrier
- 2 Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark 19711, U.S.A.; and
| | - R Jeffrey Buhr
- 3 U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, U.S.A
| | - Russell W Carlson
- 1 Complex Carbohydrate Research Center, University of Georgia, Athens 30602, U.S.A
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7
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Choma A, Komaniecka I, Zebracki K. Structure, biosynthesis and function of unusual lipids A from nodule-inducing and N 2-fixing bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:196-209. [PMID: 27836696 DOI: 10.1016/j.bbalip.2016.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 10/31/2016] [Accepted: 11/04/2016] [Indexed: 10/20/2022]
Abstract
This review focuses on the chemistry and structures of (Brady)rhizobium lipids A, indispensable parts of lipopolysaccharides. These lipids contain unusual (ω-1) hydroxylated very long chain fatty acids, which are synthesized by a very limited group of bacteria, besides rhizobia. The significance and requirement of the very long chain fatty acids for outer membrane stability as well as the genetics of the synthesis pathway are discussed. The biological role of these fatty acids for bacterial life in extremely different environments (soil and intracellular space within nodules) is also considered.
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Affiliation(s)
- Adam Choma
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Iwona Komaniecka
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Kamil Zebracki
- Department of Genetics and Microbiology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
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8
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Crespo-Rivas JC, Guefrachi I, Mok KC, Villaécija-Aguilar JA, Acosta-Jurado S, Pierre O, Ruiz-Sainz JE, Taga ME, Mergaert P, Vinardell JM. Sinorhizobium fredii HH103 bacteroids are not terminally differentiated and show altered O-antigen in nodules of the Inverted Repeat-Lacking Clade legume Glycyrrhiza uralensis. Environ Microbiol 2015; 18:2392-404. [PMID: 26521863 DOI: 10.1111/1462-2920.13101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/20/2015] [Indexed: 11/28/2022]
Abstract
In rhizobial species that nodulate inverted repeat-lacking clade (IRLC) legumes, such as the interaction between Sinorhizobium meliloti and Medicago, bacteroid differentiation is driven by an endoreduplication event that is induced by host nodule-specific cysteine rich (NCR) antimicrobial peptides and requires the participation of the bacterial protein BacA. We have studied bacteroid differentiation of Sinorhizobium fredii HH103 in three host plants: Glycine max, Cajanus cajan and the IRLC legume Glycyrrhiza uralensis. Flow cytometry, microscopy analyses and viability studies of bacteroids as well as confocal microscopy studies carried out in nodules showed that S. fredii HH103 bacteroids, regardless of the host plant, had deoxyribonucleic acid (DNA) contents, cellular sizes and survival rates similar to those of free-living bacteria. Contrary to S. meliloti, S. fredii HH103 showed little or no sensitivity to Medicago NCR247 and NCR335 peptides. Inactivation of S. fredii HH103 bacA neither affected symbiosis with Glycyrrhiza nor increased bacterial sensitivity to Medicago NCRs. Finally, HH103 bacteroids isolated from Glycyrrhiza, but not those isolated from Cajanus or Glycine, showed an altered lipopolysaccharide. Our studies indicate that, in contrast to the S. meliloti-Medicago model symbiosis, bacteroids in the S. fredii HH103-Glycyrrhiza symbiosis do not undergo NCR-induced and bacA-dependent terminal differentiation.
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Affiliation(s)
- Juan C Crespo-Rivas
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
| | - Ibtissem Guefrachi
- Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - Kenny C Mok
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - José A Villaécija-Aguilar
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain.,Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - Sebastián Acosta-Jurado
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
| | - Olivier Pierre
- Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - José E Ruiz-Sainz
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, Centre National de la Recherche Scientifique, UMR 9198, 91198, Gif-sur-Yvette, France
| | - José M Vinardell
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, CP, 41012, Sevilla, Spain
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Hold GL, Berry S, Saunders KA, Drew J, Mayer C, Brookes H, Gay NJ, El-Omar EM, Bryant CE. The TLR4 D299G and T399I SNPs are constitutively active to up-regulate expression of Trif-dependent genes. PLoS One 2014; 9:e111460. [PMID: 25365308 PMCID: PMC4218727 DOI: 10.1371/journal.pone.0111460] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/26/2014] [Indexed: 12/23/2022] Open
Abstract
Dysregulated Toll-Like Receptor (TLR) signalling and genetic polymorphisms in these proteins are linked to many human diseases. We investigated TLR4 functional variants D299G and T399I to assess the impact on LPS-induced responsiveness in comparison to wild-type TLR4. The mechanism by which this occurs in unclear as these SNPs do not lie within the lipid A binding domain or dimerisation sites of the LPS-TLR4/MD2 receptor complexes. Transfection of TLR4D299G, TLR4T399I or TLR4D299G. T399I into HEK cells resulted in constitutive activation of an NF-κB reporter gene and a blunting of the LPS-induced reporter activation compared to WT-TLR4. Unstimulated human monocyte/macrophages, from patients with the D299G and T399I SNPs demonstrated a downregulation of many genes, particularly Tram/Trif signalling pathway constitutents compared to the TLR4 wild-type subjects supporting the concept of basal receptor activity. Monocyte/macrophages from carriers of the TLR4 D299G and T399I polymorphisms stimulated with LPS showed >6 fold lower levels of NF-κB and ∼12 fold higher IFN-β gene expression levels compared to wild-type subjects (P<0.05; MWU test) and dramatically altered resultant cytokine profiles. We conclude that these TLR4 SNPs affect constitutive receptor activity which impacts on the hosts ability to respond to LPS challenge leading to a dysregulated sub-optimal immune response to infection.
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Affiliation(s)
- Georgina L. Hold
- Division of Applied Medicine, Aberdeen University, Aberdeen, United Kingdom
- * E-mail:
| | - Susan Berry
- Division of Applied Medicine, Aberdeen University, Aberdeen, United Kingdom
| | - Karin A. Saunders
- Division of Applied Medicine, Aberdeen University, Aberdeen, United Kingdom
| | - Janice Drew
- Rowett Institute of Nutrition and Health, Aberdeen University, Aberdeen, United Kingdom
| | - Claus Mayer
- Biomathematics & Statistics Scotland, Aberdeen, United Kingdom
| | - Heather Brookes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nick J. Gay
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emad M. El-Omar
- Division of Applied Medicine, Aberdeen University, Aberdeen, United Kingdom
| | - Clare E. Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Haag AF, Arnold MFF, Myka KK, Kerscher B, Dall'Angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development duringRhizobium–legume symbiosis. FEMS Microbiol Rev 2013; 37:364-83. [DOI: 10.1111/1574-6976.12003] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 09/12/2012] [Accepted: 09/14/2012] [Indexed: 01/09/2023] Open
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Chaveriat L, Gosselin I, Machut C, Martin P. Synthesis, surface tension properties and antibacterial activities of amphiphilic d -galactopyranose derivatives. Eur J Med Chem 2013; 62:177-86. [DOI: 10.1016/j.ejmech.2012.12.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 12/11/2012] [Accepted: 12/16/2012] [Indexed: 11/26/2022]
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12
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Haag AF, Arnold MFF, Myka KK, Kerscher B, Dall'Angelo S, Zanda M, Mergaert P, Ferguson GP. Molecular insights into bacteroid development duringRhizobium-legume symbiosis. FEMS Microbiol Rev 2012. [DOI: 10.1111/1574-6976.2012.12003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Andreas F. Haag
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Markus F. F. Arnold
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Kamila K. Myka
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Bernhard Kerscher
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | - Sergio Dall'Angelo
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
| | | | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique; Gif-sur-Yvette Cedex; France
| | - Gail P. Ferguson
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen; Aberdeen; UK
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13
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Vanderlinde EM, Yost CK. Genetic analysis reveals links between lipid A structure and expression of the outer membrane protein gene, ropB, in Rhizobium leguminosarum. FEMS Microbiol Lett 2012; 335:130-9. [PMID: 22845832 DOI: 10.1111/j.1574-6968.2012.02645.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/25/2012] [Accepted: 07/25/2012] [Indexed: 11/28/2022] Open
Abstract
The fabXL genes encode enzymes that synthesize the very-long-chain fatty acid - a unique acyl modification located at the 2' position of the lipid A of Gram-negative bacteria in the order Rhizobiales. Mutation of the fabXL genes causes sensitivity to outer membrane stressors and other envelope-related stresses; however, the underlying mechanisms for increased sensitivity are poorly understood. We found that expression of the outer membrane protein gene ropB is down-regulated in an acpXL mutant. Furthermore, constitutive expression of ropB in an acpXL or fabF2XL, fabF1XL mutant restores tolerance to detergents, hyperosmotic stress, and acidic pH. The fabF2XL, fabF1XL mutant also has a delayed nodulation phenotype, whereas a ropB mutant has no observable defects in nodulation, demonstrating that mutation of the fabXL genes results in pleiotropic phenotypes that can be classified as either ropB dependent or ropB independent. Ex-nodule isolates of the mutant strains display restored tolerance to detergents and hyperosmotic and acidic stress conditions; however, the rescued phenotypes are not owing to increased ropB expression. Finally, we found that the fabXL genes are induced by the sensor kinase ChvG in response to peptide-rich growth conditions, which is similar to the results reported for induction of ropB.
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14
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Ramelot TA, Rossi P, Forouhar F, Lee HW, Yang Y, Ni S, Unser S, Lew S, Seetharaman J, Xiao R, Acton TB, Everett JK, Prestegard JH, Hunt JF, Montelione GT, Kennedy MA. Structure of a specialized acyl carrier protein essential for lipid A biosynthesis with very long-chain fatty acids in open and closed conformations. Biochemistry 2012; 51:7239-49. [PMID: 22876860 DOI: 10.1021/bi300546b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.
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Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States.
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15
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Kereszt A, Mergaert P, Kondorosi E. Bacteroid development in legume nodules: evolution of mutual benefit or of sacrificial victims? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1300-9. [PMID: 21995798 DOI: 10.1094/mpmi-06-11-0152] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Symbiosomes are organelle-like structures in the cytoplasm of legume nodule cells which are composed of the special, nitrogen-fixing forms of rhizobia called bacteroids, the peribacteroid space and the enveloping peribacteroid membrane of plant origin. The formation of these symbiosomes requires a complex and coordinated interaction between the two partners during all stages of nodule development as any failure in the differentiation of either symbiotic partner, the bacterium or the plant cell prevents the subsequent transcriptional and developmental steps resulting in early senescence of the nodules. Certain legume hosts impose irreversible terminal differentiation onto bacteria. In the inverted repeat-lacking clade (IRLC) of legumes, host dominance is achieved by nodule-specific cysteine-rich peptides that resemble defensin-like antimicrobial peptides, the known effector molecules of animal and plant innate immunity. This article provides an overview on the bacteroid and symbiosome development including the terminal differentiation of bacteria in IRLC legumes as well as the bacterial and plant genes and proteins participating in these processes.
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16
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Mukhopadhya I, Hansen R, Nicholl CE, Alhaidan YA, Thomson JM, Berry SH, Pattinson C, Stead DA, Russell RK, El-Omar EM, Hold GL. A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease. PLoS One 2011; 6:e27076. [PMID: 22073125 PMCID: PMC3205041 DOI: 10.1371/journal.pone.0027076] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 10/09/2011] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD) arises in genetically susceptible individuals as a result of an unidentified environmental trigger, possibly a hitherto unknown bacterial pathogen. Twenty-six clinical isolates of Sutterella wadsworthensis were obtained from 134 adults and 61 pediatric patients undergoing colonoscopy, of whom 69 and 29 respectively had IBD. S. wadsworthensis was initially more frequently isolated from IBD subjects, hence this comprehensive study was undertaken to elucidate its role in IBD. Utilizing these samples, a newly designed PCR was developed, to study the prevalence of this bacterium in adult patients with ulcerative colitis (UC). Sutterella wadsworthensis was detected in 83.8% of adult patients with UC as opposed to 86.1% of control subjects (p = 0.64). Selected strains from IBD cases and controls were studied to elicit morphological, proteomic, genotypic and pathogenic differences. This study reports Scanning Electron Microscopy (SEM) appearances and characteristic MALDI-TOF MS protein profiles of S. wadsworthensis for the very first time. SEM showed that the bacterium is pleomorphic, existing in predominantly two morphological forms, long rods and coccobacilli. No differences were noted in the MALDI-TOF mass spectrometry proteomic analysis. There was no distinct clustering of strains identified from cases and controls on sequence analysis. Cytokine response after monocyte challenge with strains from patients with IBD and controls did not yield any significant differences. Our studies indicate that S. wadsworthensis is unlikely to play a role in the pathogenesis of IBD. Strains from cases of IBD could not be distinguished from those identified from controls.
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Affiliation(s)
- Indrani Mukhopadhya
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Richard Hansen
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
- Child Health, University of Aberdeen, Royal Aberdeen Children's Hospital, Foresterhill, Aberdeen, United Kingdom
| | - Charlotte E. Nicholl
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Yazeid A. Alhaidan
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - John M. Thomson
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Susan H. Berry
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Craig Pattinson
- Aberdeen Proteomics Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - David A. Stead
- Aberdeen Proteomics Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Richard K. Russell
- Department of Paediatric Gastroenterology, Royal Hospital for Sick Children, Glasgow, United Kingdom
| | - Emad M. El-Omar
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Georgina L. Hold
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
- * E-mail: .
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17
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A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease. PLoS One 2011. [PMID: 22073125 DOI: 10.1371/journal.pone.0027076.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inflammatory bowel disease (IBD) arises in genetically susceptible individuals as a result of an unidentified environmental trigger, possibly a hitherto unknown bacterial pathogen. Twenty-six clinical isolates of Sutterella wadsworthensis were obtained from 134 adults and 61 pediatric patients undergoing colonoscopy, of whom 69 and 29 respectively had IBD. S. wadsworthensis was initially more frequently isolated from IBD subjects, hence this comprehensive study was undertaken to elucidate its role in IBD. Utilizing these samples, a newly designed PCR was developed, to study the prevalence of this bacterium in adult patients with ulcerative colitis (UC). Sutterella wadsworthensis was detected in 83.8% of adult patients with UC as opposed to 86.1% of control subjects (p = 0.64). Selected strains from IBD cases and controls were studied to elicit morphological, proteomic, genotypic and pathogenic differences. This study reports Scanning Electron Microscopy (SEM) appearances and characteristic MALDI-TOF MS protein profiles of S. wadsworthensis for the very first time. SEM showed that the bacterium is pleomorphic, existing in predominantly two morphological forms, long rods and coccobacilli. No differences were noted in the MALDI-TOF mass spectrometry proteomic analysis. There was no distinct clustering of strains identified from cases and controls on sequence analysis. Cytokine response after monocyte challenge with strains from patients with IBD and controls did not yield any significant differences. Our studies indicate that S. wadsworthensis is unlikely to play a role in the pathogenesis of IBD. Strains from cases of IBD could not be distinguished from those identified from controls.
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18
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Haag AF, Baloban M, Sani M, Kerscher B, Pierre O, Farkas A, Longhi R, Boncompagni E, Hérouart D, Dall’Angelo S, Kondorosi E, Zanda M, Mergaert P, Ferguson GP. Protection of Sinorhizobium against host cysteine-rich antimicrobial peptides is critical for symbiosis. PLoS Biol 2011; 9:e1001169. [PMID: 21990963 PMCID: PMC3186793 DOI: 10.1371/journal.pbio.1001169] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 08/22/2011] [Indexed: 01/01/2023] Open
Abstract
A bacterial membrane protein, BacA, protects Sinorhizobium meliloti against the antimicrobial activity of host peptides, enabling the peptides to induce bacterial persistence rather than bacterial death. Sinorhizobium meliloti differentiates into persisting, nitrogen-fixing bacteroids within root nodules of the legume Medicago truncatula. Nodule-specific cysteine-rich antimicrobial peptides (NCR AMPs) and the bacterial BacA protein are essential for bacteroid development. However, the bacterial factors central to the NCR AMP response and the in planta role of BacA are unknown. We investigated the hypothesis that BacA is critical for the bacterial response towards NCR AMPs. We found that BacA was not essential for NCR AMPs to induce features of S. meliloti bacteroids in vitro. Instead, BacA was critical to reduce the amount of NCR AMP-induced membrane permeabilization and bacterial killing in vitro. Within M. truncatula, both wild-type and BacA-deficient mutant bacteria were challenged with NCR AMPs, but this resulted in persistence of the wild-type bacteria and rapid cell death of the mutant bacteria. In contrast, BacA was dispensable for bacterial survival in an M. truncatula dnf1 mutant defective in NCR AMP transport to the bacterial compartment. Therefore, BacA is critical for the legume symbiosis by protecting S. meliloti against the bactericidal effects of NCR AMPs. Host AMPs are ubiquitous in nature and BacA proteins are essential for other chronic host infections by symbiotic and pathogenic bacteria. Hence, our findings suggest that BacA-mediated protection of bacteria against host AMPs is a critical stage in the establishment of different prolonged host infections. Certain bacterial species have the unique capacity to enter into eukaryotic host cells and establish prolonged infections, which can be beneficial (e.g. bacterial-legume symbiosis) or detrimental (e.g. chronic disease) for the host. However, the mechanisms by which bacteria persist in host cells are poorly understood. Legume peptides and the bacterial BacA membrane protein play essential roles in enabling bacteria to establish prolonged legume infections. However, the biological function of BacA in persistent legume infections has eluded scientists for nearly two decades. In this article, we investigated a potential relationship between legume peptides and BacA in the establishment of prolonged bacterial-legume infections. We found that BacA was critical to protect bacteria against the antimicrobial action of legume peptides, thereby allowing the peptides to induce bacterial persistence within the legume rather than rapid bacterial death. Mammalian hosts also produce peptides in response to invading microorganisms and BacA proteins are critical for medically important bacterial pathogens such as Mycobacterium tuberculosis to form prolonged mammalian infections. Therefore, our results suggest that BacA-mediated protection against host peptides might be a conserved mechanism used by both symbiotic and pathogenic bacterial species to establish long-term host infections.
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Affiliation(s)
- Andreas F. Haag
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Mikhail Baloban
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - Monica Sani
- Consiglio Nazionale delle Ricerche–Istituto di Chimica del Riconoscimento Molecolare C.N.R.-I.C.R.M., Milano, Italy
- KemoTech s.r.l., Pula, Italy
| | - Bernhard Kerscher
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Olivier Pierre
- Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Nice–Sophia Antipolis, Sophia-Antipolis, France
| | - Attila Farkas
- Institute for Plant Genomics, Human Biotechnology and Bioenergy, Bay Zoltan Foundation for Applied Research, Szeged, Hungary
| | - Renato Longhi
- Consiglio Nazionale delle Ricerche–Istituto di Chimica del Riconoscimento Molecolare C.N.R.-I.C.R.M., Milano, Italy
| | - Eric Boncompagni
- Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Nice–Sophia Antipolis, Sophia-Antipolis, France
| | - Didier Hérouart
- Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Nice–Sophia Antipolis, Sophia-Antipolis, France
| | - Sergio Dall’Angelo
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Eva Kondorosi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Matteo Zanda
- Consiglio Nazionale delle Ricerche–Istituto di Chimica del Riconoscimento Molecolare C.N.R.-I.C.R.M., Milano, Italy
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- * E-mail: (PM); (GPF)
| | - Gail P. Ferguson
- School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail: (PM); (GPF)
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